Dataset Summary

• Study Reference: PMID: 35623341
  
• Clinical Trial: ISPY2/NCT01042379
  
• Data Source: GEO: GSE194040
  
• Study Population:
  • Genomics Data: 987 patients (mRNA & RPPA profiling)
    
  • Radiomics Data: 985 patients (MRI scans)
    
• Platforms Used:
  • Genomics: Agilent 44K arrays
    
  • Radiomics: MRI (DCE-MRI)

Patient and Treatment Details

• Total Patients (RNA-seq): 987
  
• Total Patients (MRI): 985 (719 I-SPY2 cases, 266 ACRIN-6698 cases)
  
• Treatment Groups:
  • IO + Chemo: 69 patients
    
  • Chemo + Targeted Therapy: 687 patients
    
  • Chemo Alone: 179 patients
    
  • Targeted Therapy Alone: 52 patients
    
• Key Treatment Arms:
  • Paclitaxel ± Trastuzumab
    
  • Veliparib + Carboplatin
    
  • AMG-386 (Trebananib) ± Trastuzumab
    
  • Neratinib, Ganetespib, Ganitumab, Pembrolizumab, Pertuzumab, T-DM1

Additional Information

• Batch Correction:
  • ComBat was applied to correct batch effects in gene expression data.
    
  • Adjusted ~800 patients; linear adjustments applied to remaining cases.
• Radiomics Data:
  • MRI dataset includes 4 serial DCE-MRI scans per patient.
    
  • Performed before and during neoadjuvant chemotherapy to track tumor volume changes and response.
• Data Availability:
  • 📂 Genomics: Available in GEO: GSE194040.
    
  • 📂 Imaging: MRI datasets accessible via The Cancer Imaging Archive (ISPY2 Collection).
• Key Reference:
  • Wolf DM et al., Cancer Cell, 2022. PMID: 35623341.

Load Required Libraries

library(here)
library(MultiAssayExperiment) 
library(knitr)
library(readxl)
library(ggplot2)
library(dplyr)
library(tidyr)
library(ggvenn)
library(kableExtra) 
library(limma)
library(limma)
library(EnhancedVolcano)
library(msigdbr)
library(fgsea)